1. The Structure and Function of Large Biological Molecules
Chapter 5
The Structure and Function of Large Biological Molecules

2. Overview: The Molecules of Life
All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids
Within cells, small organic molecules are joined together to form larger molecules
Macromolecules are large molecules composed of thousands of covalently connected atoms
Molecular structure and function are inseparable
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3. Fig. 5-1
Figure 5.1 Why do scientists study the structures of macromolecules?

4. Concept 5.1: Macromolecules are polymers, built from monomers
These small building-block molecules are called monomers
A polymer is a long molecule consisting of many similar building blocks
Three of the four classes of life’s organic molecules are polymers:
Carbohydrates
Proteins
Nucleic acids
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5. The Synthesis and Breakdown of Polymers
A condensation reaction or more specifically a dehydration reaction occurs when two monomers bond together through the loss of a water molecule
Enzymes are macromolecules that speed up the dehydration process
Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction
Animation: Polymers
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6. Dehydration removes a water molecule, forming a new bond H2O
Fig. 5-2a HO 1 2 3 H HO H
Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
H2O
Figure 5.2 The synthesis and breakdown of polymers HO 1 2 3 4 H
Longer polymer
(a)
Dehydration reaction in the synthesis of a polymer

7. HO 1 2 3 4 H H2O HO 1 2 3 H HO H (b) Hydrolysis adds a water
Fig. 5-2b HO 1 2 3 4 H
Hydrolysis adds a water
molecule, breaking a bond
H2O
Figure 5.2 The synthesis and breakdown of polymers HO 1 2 3 H HO H
(b)
Hydrolysis of a polymer

8. Glucose (C6H12O6) is the most common monosaccharide
Sugars
Monosaccharides have molecular formulas that are usually multiples of CH2O
Glucose (C6H12O6) is the most common monosaccharide
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9. Though often drawn as linear skeletons, in aqueous solutions many sugars form rings
Monosaccharides serve as a major fuel for cells and as raw material for building molecules
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10. (a) Linear and ring forms (b) Abbreviated ring structure
Fig. 5-4
(a) Linear and ring forms
Figure 5.4 Linear and ring forms of glucose
(b) Abbreviated ring structure

11. Animation: Disaccharides
A disaccharide is formed when a dehydration reaction joins two monosaccharides
This covalent bond is called a glycosidic linkage
Animation: Disaccharides
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12. (a) Dehydration reaction in the synthesis of maltose
Fig. 5-5
1–4
glycosidic
linkage
Glucose
Glucose
Maltose
(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
linkage
Figure 5.5 Examples of disaccharide synthesis
Glucose
Fructose
Sucrose
(b) Dehydration reaction in the synthesis of sucrose

13. Storage Polysaccharides
Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
Plants store surplus starch as granules within chloroplasts and other plastids
Glycogen is a storage polysaccharide in animals
Humans and other vertebrates store glycogen mainly in liver and muscle cells
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14. (a) Starch: a plant polysaccharide
Fig. 5-6
Chloroplast
Starch
Mitochondria
Glycogen granules
0.5 µm
1 µm
Figure 5.6 Storage polysaccharides of plants and animals
Amylose
Glycogen
Amylopectin
(a) Starch: a plant polysaccharide
(b) Glycogen: an animal polysaccharide

15. Structural Polysaccharides
The polysaccharide cellulose is a major component of the tough wall of plant cells
Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
The difference is based on two ring forms for glucose: alpha () and beta ()
Animation: Polysaccharides
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16. (a)  and  glucose ring structures
Fig. 5-7a
 Glucose
 Glucose
Figure 5.7 Starch and cellulose structures
(a)  and  glucose ring structures

17. (b) Starch: 1–4 linkage of  glucose monomers
Fig. 5-7bc
(b) Starch: 1–4 linkage of  glucose monomers
Figure 5.7 Starch and cellulose structures
(c) Cellulose: 1–4 linkage of  glucose monomers

18. Cell walls Cellulose microfibrils in a plant cell wall Microfibril
Fig. 5-8
Cell walls
Cellulose
microfibrils
in a plant
cell wall
Microfibril
10 µm
0.5 µm
Cellulose
molecules
Figure 5.8 The arrangement of cellulose in plant cell walls
Glucose
monomer

19. Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose
Cellulose in human food passes through the digestive tract as insoluble fiber. Irritates the lining of the digestive system, causing more frequent bowel movements and preventing constipation. “roughage”
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20. Some microbes use enzymes to digest cellulose
Fig. 5-9
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have symbiotic relationships with these microbes
Figure 5.9 Cellulose-digesting prokaryotes are found in grazing animals such as this cow

21. Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods
Chitin also provides structural support for the cell walls of many fungi
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22. (a) The structure of the chitin monomer. (b) (c) Chitin forms the
Fig. 5-10
(a)
The structure
of the chitin
monomer.
(b)
Chitin forms the
exoskeleton of
arthropods.
(c)
Chitin is used to make
a strong and flexible
surgical thread.
Figure 5.10 Chitin, a structural polysaccharide

23. Concept 5.3: Lipids are a diverse group of hydrophobic molecules
Lipids are the one class of large biological molecules that do not form polymers
The unifying feature of lipids is having little or no affinity for water (hydrophobic)
The most biologically important lipids are fats, phospholipids, and steroids
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24. Fats
Fats are constructed from two types of smaller molecules: glycerol and fatty acids
Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon
A fatty acid consists of a carboxyl group attached to a long carbon skeleton
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25. Fatty acid (palmitic acid)
Fig. 5-11
Fatty acid
(palmitic acid)
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
Figure 5.11 The synthesis and structure of a fat, or triacylglycerol
(b) Fat molecule (triacylglycerol)

26. Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats
In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
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27. Unsaturated fatty acids have one or more double bonds
Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
Unsaturated fatty acids have one or more double bonds
Animation: Fats
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28. Structural formula of a saturated fat molecule Stearic acid, a
Fig. 5-12a
Structural
formula of a
saturated fat
molecule
Figure 5.12 Examples of saturated and unsaturated fats and fatty acids
Stearic acid, a
saturated fatty
acid
(a)
Saturated fat

29. unsaturated fatty acid Oleic acid, an cis double bond causes bending
Fig. 5-12b
Structural formula
of an unsaturated
fat molecule
Oleic acid, an
unsaturated
fatty acid
Figure 5.12 Examples of saturated and unsaturated fats and fatty acids
cis double
bond causes
bending
(b)
Unsaturated fat

30. Most animal fats are saturated
Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature
Most animal fats are saturated
Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature
Plant fats and fish fats are usually unsaturated
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31. Hydrogenating vegetable oils also creates trans fats
A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen
Hydrogenating vegetable oils also creates trans fats
These trans fats may contribute more than saturated fats to cardiovascular disease
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32. The major function of fats is energy storage
Humans and other mammals store their fat in adipose cells
Adipose tissue also cushions vital organs and insulates the body
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33. Phospholipids
In a phospholipid, two fatty acids and a phosphate group are attached to glycerol
The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head
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34. Choline Hydrophilic head Phosphate Glycerol Fatty acids
Fig. 5-13
Choline
Hydrophilic head
Phosphate
Glycerol
Fatty acids
Hydrophobic tails
Hydrophilic
head
Figure 5.13 The structure of a phospholipid
Hydrophobic
tails
(a)
Structural formula
(b)
Space-filling model
(c)
Phospholipid symbol

35. Phospholipids are the major component of all cell membranes
When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior
The structure of phospholipids results in a bilayer arrangement found in cell membranes
Phospholipids are the major component of all cell membranes
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36. Hydrophilic head Hydrophobic tail WATER WATER Fig. 5-14
Figure 5.14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment
Hydrophobic
tail
WATER

37. Steroids
Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
Cholesterol, an important steroid, is a component in animal cell membranes
Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease
For the Cell Biology Video Space Filling Model of Cholesterol, go to Animation and Video Files.
For the Cell Biology Video Stick Model of Cholesterol, go to Animation and Video Files.
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38. Fig. 5-15
Figure 5.15 Cholesterol, a steroid

39. Proteins account for more than 50% of the dry mass of most cells
Concept 5.4: Proteins have many structures, resulting in a wide range of functions
Proteins account for more than 50% of the dry mass of most cells
Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances
PROTEINS ARE THE ONLY MOLECULE DIRECTLY ENCODED FOR BY DNA!!!
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40. Table 5-1
Table 5-1

41. Animation: Structural Proteins
Animation: Storage Proteins
Animation: Transport Proteins
Animation: Receptor Proteins
Animation: Contractile Proteins
Animation: Defensive Proteins
Animation: Hormonal Proteins
Animation: Sensory Proteins
Animation: Gene Regulatory Proteins
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42. Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions
Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life
Animation: Enzymes
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43. Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O
Fig. 5-16
Substrate
(sucrose)
Glucose
Enzyme
(sucrase) OH
H2O
Fructose
Figure 5.16 The catalytic cycle of an enzyme H O

44. Polypeptides are polymers built from the same set of 20 amino acids
A protein consists of one or more polypeptides
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45. Amino acids are organic molecules with carboxyl and amino groups
Amino Acid Monomers
Amino acids are organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side chains, called R groups
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46. Diverse as proteins are, they are all _1___________ constructed from the same set of _2_________ amino acids. Polymers of amino acids are called __3_______________ . A __4___________ consists of one or more polypeptides folded and coiled into a _5_______________ stucture.
polymers 20
polypeptides
protein
Three-dimensional

47. Fig. 5-UN1
 carbon
Amino
group
Carboxyl
group

48. Amino acids are linked by peptide bonds
Amino Acid Polymers
Amino acids are linked by peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few to more than a thousand monomers
Each polypeptide has a unique linear sequence of amino acids
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49. Amino end (N-terminus) Carboxyl end (C-terminus)
Fig. 5-18
Peptide
bond
(a)
Side chains
Peptide
bond
Figure 5.18 Making a polypeptide chain
Backbone
Amino end
(N-terminus)
Carboxyl end
(C-terminus)
(b)

50. Protein Structure and Function
A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape
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51. Sickle-Cell Disease: A Change in Primary Structure
A slight change in primary structure can affect a protein’s structure and ability to function
Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
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52. A protein’s structure determines its function
The sequence of amino acids determines a protein’s three-dimensional structure
A protein’s structure determines its function
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53. Fig. 5-22
Normal hemoglobin
Sickle-cell hemoglobin
Primary
structure
Primary
structure
Val
His
Leu
Thr
Pro
Glu
Glu
Val
His
Leu
Thr
Pro
Val
Glu 1 2 3 4 5 6 7 1 2 3 4 5 6 7
Exposed
hydrophobic
region
Secondary
and tertiary
structures
Secondary
and tertiary
structures
 subunit
 subunit    
Quaternary
structure
Normal
hemoglobin
(top view)
Quaternary
structure
Sickle-cell
hemoglobin    
Function
Molecules do
not associate
with one
another; each
carries oxygen.
Function
Molecules
interact with
one another and
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
Figure 5.22 A single amino acid substitution in a protein causes sickle-cell disease
10 µm
10 µm
Red blood
cell shape
Normal red blood
cells are full of
individual
hemoglobin
moledules, each
carrying oxygen.
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
red blood cell into
sickle shape.

54. 10 µm 10 µm Normal red blood cells are full of individual hemoglobin
Fig. 5-22c
10 µm
10 µm
Normal red blood
cells are full of
individual
hemoglobin
molecules, each
carrying oxygen.
Fibers of abnormal
hemoglobin deform
red blood cell into
sickle shape.
Figure 5.22 A single amino acid substitution in a protein causes sickle-cell disease

55. A ribbon model of lysozyme A space-filling model of lysozyme
Fig. 5-19
Groove
Groove
Figure 5.19 Structure of a protein, the enzyme lysozyme
(a)
A ribbon model of lysozyme
(b)
A space-filling model of lysozyme

56. Antibody protein Protein from flu virus
Fig. 5-20
Antibody protein
Protein from flu virus
Figure 5.20 An antibody binding to a protein from a flu virus

57. Four Levels of Protein Structure
The primary structure of a protein is its unique sequence of amino acids
Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain
Tertiary structure is determined by interactions among various side chains (R groups)
Quaternary structure results when a protein consists of multiple polypeptide chains
Animation: Protein Structure Introduction
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58. Figure 5.21 Levels of protein structure—primary structure
Secondary
Structure
Tertiary
Structure
Quaternary
Structure
 pleated sheet
+H3N
Amino end
Examples of
amino acid
subunits
 helix
Figure 5.21 Levels of protein structure—primary structure

59. Animation: Primary Protein Structure
Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word
Primary structure is determined by inherited genetic information
Animation: Primary Protein Structure
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60. +H3N Primary Structure Amino end Amino acid subunits 1 5 10 15 20 25
Fig. 5-21a
Primary Structure 1 5
+H3N
Amino end 10
Amino acid
subunits 15
Figure 5.21 Levels of protein structure—primary structure 20 25

61. Animation: Secondary Protein Structure
The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone
Typical secondary structures are a coil called an  helix and a folded structure called a  pleated sheet
For the Cell Biology Video An Idealized Alpha Helix: No Sidechains, go to Animation and Video Files.
For the Cell Biology Video An Idealized Alpha Helix, go to Animation and Video Files.
For the Cell Biology Video An Idealized Beta Pleated Sheet Cartoon, go to Animation and Video Files.
For the Cell Biology Video An Idealized Beta Pleated Sheet, go to Animation and Video Files.
Animation: Secondary Protein Structure
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62. Secondary Structure  pleated sheet Examples of amino acid subunits
Fig. 5-21c
Secondary Structure
 pleated sheet
Examples of
amino acid
subunits
Figure 5.21 Levels of protein structure—secondary structure
 helix

63. Abdominal glands of the spider secrete silk fibers
Fig. 5-21d
Abdominal glands of the
spider secrete silk fibers
made of a structural protein
containing  pleated sheets.
The radiating strands, made
of dry silk fibers, maintain
the shape of the web.
Figure 5.21 Levels of protein structure—secondary structure
The spiral strands (capture
strands) are elastic, stretching
in response to wind, rain,
and the touch of insects.

64. Animation: Tertiary Protein Structure
Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents
These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions
Strong covalent bonds called disulfide bridges may reinforce the protein’s structure
Animation: Tertiary Protein Structure
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65. Tertiary Structure Quaternary Structure
Fig. 5-21e
Tertiary Structure
Quaternary Structure
Figure 5.21 Levels of protein structure—tertiary and quaternary structures

66. Polypeptide  Chains chain Iron Heme  Chains Hemoglobin Collagen
Fig. 5-21g
Polypeptide
chain
 Chains
Iron
Figure 5.21 Levels of protein structure—tertiary and quaternary structures
Heme
 Chains
Hemoglobin
Collagen

67. Animation: Quaternary Protein Structure
Quaternary structure results when two or more polypeptide chains form one macromolecule
Collagen is a fibrous protein consisting of three polypeptides coiled like a rope
Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains
Animation: Quaternary Protein Structure
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68. What Determines Protein Structure?
In addition to primary structure, physical and chemical conditions can affect structure
Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel
This loss of a protein’s native structure is called denaturation
A denatured protein is biologically inactive
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69. Denaturation Normal protein Denatured protein Renaturation Fig. 5-23
Figure 5.23 Denaturation and renaturation of a protein
Normal protein
Denatured protein
Renaturation

70. Concept 5.5: Nucleic acids store and transmit hereditary information
The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
Genes are made of DNA, a nucleic acid
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71. The Roles of Nucleic Acids
There are two types of nucleic acids:
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
Protein synthesis occurs in ribosomes
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72. DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM
Fig
DNA 1
Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
Figure 5.26 DNA → RNA → protein

73. DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2
Fig
DNA 1
Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA 2
Movement of
mRNA into cytoplasm
via nuclear pore
Figure 5.26 DNA → RNA → protein

74. DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2
Fig
DNA 1
Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA 2
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
Figure 5.26 DNA → RNA → protein 3
Synthesis
of protein
Amino
acids
Polypeptide

75. The Structure of Nucleic Acids
Nucleic acids are polymers called polynucleotides
Each polynucleotide is made of monomers called nucleotides
Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group
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76. (a) Polynucleotide, or nucleic acid (c) Nucleoside components: sugars
Fig. 5-27
5 end
Nitrogenous bases
Pyrimidines
5C
3C
Nucleoside
Nitrogenous
base
Cytosine (C)
Thymine (T, in DNA)
Uracil (U, in RNA)
Purines
Phosphate
group
Sugar
(pentose)
5C
Adenine (A)
Guanine (G)
3C
(b) Nucleotide
Sugars
3 end
Figure 5.27 Components of nucleic acids
(a) Polynucleotide, or nucleic acid
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars

77. (c) Nucleoside components: nitrogenous bases
Fig. 5-27c-1
Nitrogenous bases
Pyrimidines
Cytosine (C)
Thymine (T, in DNA)
Uracil (U, in RNA)
Purines
Figure 5.27 Components of nucleic acids
Adenine (A)
Guanine (G)
(c) Nucleoside components: nitrogenous bases

78. (c) Nucleoside components: sugars
Fig. 5-27c-2
Sugars
Deoxyribose (in DNA)
Ribose (in RNA)
Figure 5.27 Components of nucleic acids
(c) Nucleoside components: sugars

79. The DNA Double Helix
A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix
In the DNA double helix, the two backbones run in opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel
One DNA molecule includes many genes
The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
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80. Nitrogenous base Phosphate group Sugar (pentose)
Fig. 5-27ab
5' end
5'C
3'C
Nucleoside
Nitrogenous
base
5'C
Phosphate
group
Figure 5.27 Components of nucleic acids
3'C
Sugar
(pentose)
5'C
3'C
(b) Nucleotide
3' end
(a) Polynucleotide, or nucleic acid

81. 5' end 3' end Sugar-phosphate backbones Base pair (joined by
Fig. 5-28
5' end
3' end
Sugar-phosphate
backbones
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
3' end
Figure 5.28 The DNA double helix and its replication
5' end
New
strands
5' end
3' end
5' end
3' end

82. DNA and Proteins as Tape Measures of Evolution
The linear sequences of nucleotides in DNA molecules are passed from parents to offspring
Two closely related species are more similar in DNA than are more distantly related species
Molecular biology can be used to assess evolutionary kinship
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83. The Theme of Emergent Properties in the Chemistry of Life: A Review
Higher levels of organization result in the emergence of new properties
Organization is the key to the chemistry of life
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84. Fig. 5-UN2

85. Fig. 5-UN2a

86. Fig. 5-UN2b

87. 100 % of glycosidic linkages broken 50 Time
Fig. 5-UN3
100
% of glycosidic
linkages broken 50
Time

88. Fig. 5-UN9

89. You should now be able to:
List and describe the four major classes of molecules
Describe the formation of a glycosidic linkage and distinguish between monosaccharides, disaccharides, and polysaccharides
Distinguish between saturated and unsaturated fats and between cis and trans fat molecules
Describe the four levels of protein structure
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90. You should now be able to:
Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, the 5 end and 3 end of a nucleotide
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